VMD-L Mailing List

From: Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Tue Nov 29 2005 - 04:46:38 CST

Good to know. I don't work at all with this patch, but it's still useful
:). I don't think that reassigning charges will be a big issue, though.
You can "easily" do it using Gaussian, for example. However, I think
that you can use the CT3 patch with no problem for you system (this one
is standard for NMR experiments).

Good luck!
Michel

-----Original Message-----
From: hodak_at_chips.ncsu.edu [mailto:hodak_at_chips.ncsu.edu]
Sent: Tuesday, November 29, 2005 3:22 AM
To: Jim Phillips
Cc: Michel Espinoza-Fonseca; vmd-l_at_ks.uiuc.edu
Subject: RE: vmd-l: Uncharged terminal ends?

Thanks for explanation, I now understand what the problem is. I looked
at
all the residues and the only exception that does not have HA atom is
GLY,
so CT1 should presumably work for everything except GLY.

Good to finally know what is going on, why my toy HIS-GLY system, the
first thing I threw at vmd, was not working.

On Mon, 28 Nov 2005, Jim Phillips wrote:

> Hi folks,
>
> The patch CT1 looks like this:
>
> PRES CT1 0.00 ! methylated C-terminus from methyl acetate
> GROUP ! use in generate statement
> ATOM N NH1 -0.47 !
> ATOM HN H 0.31 ! OT1
> ATOM CA CT1 0.17 ! | //
> ATOM HA HB 0.09 ! -N--CA--C HT1
> ATOM C CD 0.63 ! | | \ /
> ATOM OT1 OB -0.52 ! HN HA OT2--CT--HT2
> ATOM OT2 OS -0.34 ! \
> ATOM CT CT3 -0.14 ! HT3
> ATOM HT1 HA 0.09 !
> ATOM HT2 HA 0.09 !
> ATOM HT3 HA 0.09 !
> DELETE ATOM O
> ...
>
> Most residues, like ALA below, this would be fine for:
>
> RESI ALA 0.00
> GROUP
> ATOM N NH1 -0.47 ! |
> ATOM HN H 0.31 ! HN-N
> ATOM CA CT1 0.07 ! | HB1
> ATOM HA HB 0.09 ! | /
> GROUP ! HA-CA--CB-HB2
> ATOM CB CT3 -0.27 ! | \
> ATOM HB1 HA 0.09 ! | HB3
> ATOM HB2 HA 0.09 ! O=C
> ATOM HB3 HA 0.09 ! |
> GROUP !
> ATOM C C 0.51
> ATOM O O -0.51
> ...
>
> For ALA, the CT1 line "ATOM HA HB" changes the type/charge of the
existing
> atom HA (or it would if they weren't the same already).
>
> The sequence is just HIS GLY, so the C-terminal residue is GLY:
>
> RESI GLY 0.00
> GROUP
> ATOM N NH1 -0.47 ! |
> ATOM HN H 0.31 ! N-H
> ATOM CA CT2 -0.02 ! |
> ATOM HA1 HB 0.09 ! |
> ATOM HA2 HB 0.09 ! HA1-CA-HA2
> GROUP ! |
> ATOM C C 0.51 ! |
> ATOM O O -0.51 ! C=O
> ! |
> ...
>
> In this case, the CT1 line "ATOM HA HB" adds a *new* atom, HA, which
is
> just wrong. You could delete that line and things would be better,
but
> you'd still get the angle parameter error because CT1 line "ATOM CA
CT1"
> changes the type of the GLY CA from CT2 to CT1 (which, I am guessing,
is
> wrong for an atom bonded to two hydrogens) so you get an HB-CT1-HB
> parameter error (you're asking for something that shouldn't exist).
>
> You could easily modify the CT1 patch to use the correct atom types,
but
> getting the charges right is beyond my expertise.
>
> -Jim
>
>
> On Tue, 22 Nov 2005, hodak_at_chips.ncsu.edu wrote:
>
> > Generated protein looks much better now, but only if last is set to
CT3.
> > CT1 (which I like since it is simple) still generates broken pdb
file (and
> > namd complains about the HB CT1 HB angle). Do you know what the
problem
> > with CT1 is?
> >
> > Also, even with CT3 namd still complain about non-unique
coordinates,
> > but all coordinates seem to be OK. Perhaps the problem is with namd
> > config file, but I first want to psfgen and CT1 (if possible)
running.
> >
> > Thanks a lot for your help.
> > Miro
> >
> > On Tue, 22 Nov 2005, Michel Espinoza-Fonseca wrote:
> >
> >> okay, I think that now it'll work... I modified a little bit the
input script for psfgen. The script is:
> >>
> >> topology top_all27_prot_na.inp
> >> alias residue HIS HSE
> >> segment HG3 {pdb HG3.pdb
> >> first ACE
> >> last CT3
> >> auto angles dihedrals}
> >> coordpdb HG3.pdb HG3
> >> guesscoord
> >> writepdb HG3-good.pdb
> >> writepsf HG3-good.psf
> >>
> >> you have to be sure that the protonation state of HIS is correct
(HSD, HSE or HSP). I just changed "auto none" by "auto angles dihedrals"
to actually reassing angles and dihedrals. hopefully you won't have
problems now.
> >>
> >> I also attach the pdb and psf files I got.
> >>
> >> Cheers,
> >> Michel
> >>
> >> ________________________________
> >>
> >> From: hodak_at_chips.ncsu.edu [mailto:hodak_at_chips.ncsu.edu]
> >> Sent: Tue 11/22/2005 5:13 AM
> >> To: Michel Espinoza-Fonseca
> >> Cc: vmd-l_at_ks.uiuc.edu
> >> Subject: RE: vmd-l: Uncharged terminal ends?
> >>
> >>
> >>
> >> I stripped all hydrogens from my starting dipeptide (HG) but the
problem
> >> is still there (namd still complains). I cannot spot the atoms that
are
> >> close or identitical, but 27th atom has 0,0,0 coordinates. I am
attachaing
> >> my starting pdb file and also the script I am using.
> >>
> >> Thanks,
> >> Miro
> >>
> >> On Tue, 22 Nov 2005, Michel Espinoza-Fonseca wrote:
> >>
> >>> okay... I have one more question... Is your starting protein
WITHOUT hydrogen atoms? if yes, remove all of them prior building your
psf and pdb files. You can also check that the structure of your protein
is correct (e.g., that you don't have duplicated atoms).
> >>>
> >>> Try to do that and tell me if you see something weird. You can
also send me your pdb file and I can check it.
> >>>
> >>> Cheers,
> >>> Michel
> >>>
> >>> ________________________________
> >>>
> >>> From: hodak_at_chips.ncsu.edu [mailto:hodak_at_chips.ncsu.edu]
> >>> Sent: Tue 11/22/2005 4:40 AM
> >>> To: Michel Espinoza-Fonseca
> >>> Cc: vmd-l_at_ks.uiuc.edu
> >>> Subject: RE: vmd-l: Uncharged terminal ends?
> >>>
> >>>
> >>>
> >>> It seems that I have one more issue with generated pdb file. When
I run
> >>> namd I get:
> >>> Warning: Not all atoms have unique coordinates.
> >>>
> >>> Inspecting generated pdb file, my CA on G has two hydrogen that
are very
> >>> close (and CA actually has 5 bonds):
> >>>
> >>> ATOM 27 HA GLY 3 4.826 -0.964 -1.247 1.00 0.00
PROT H
> >>> ATOM 36 HA2 GLY 3 4.806 -0.987 -1.255 0.00 0.00
PROT H
> >>>
> >>> Please note that 36 is my last atom.
> >>> It seems like problem with psfgen's guessing of coordinates
(guesscoord).
> >>>
> >>> What can I do to avoid this problem?
> >>>
> >>> Thanks,
> >>> Miro
> >>>
> >>> On Tue, 22 Nov 2005, Michel Espinoza-Fonseca wrote:
> >>>
> >>>> "auto none" automatically generates angles and dihedrals based on
bonds, since the topology file don't list angles and dihedrals. This is
specially needed when you apply patches on your protein (such as ACE or
CT1) or with water.
> >>>>
> >>>> Hope it is clear,
> >>>> Michel
> >>>>
> >>>> ________________________________
> >>>>
> >>>> From: hodak_at_chips.ncsu.edu [mailto:hodak_at_chips.ncsu.edu]
> >>>> Sent: Tue 11/22/2005 4:16 AM
> >>>> To: Michel Espinoza-Fonseca
> >>>> Cc: vmd-l_at_ks.uiuc.edu
> >>>> Subject: RE: vmd-l: Uncharged terminal ends?
> >>>>
> >>>>
> >>>>
> >>>> With this I am namd simulation will start. Now what is does "auto
none"
> >>>> actually do?
> >>>>
> >>>> Thanks,
> >>>> Miro
> >>>>
> >>>> On Tue, 22 Nov 2005, Michel Espinoza-Fonseca wrote:
> >>>>
> >>>>> mmmm... try to rebuild your system using
> >>>>>
> >>>>> first ACE
> >>>>> last CT1
> >>>>> auto none
> >>>>>
> >>>>> and then see if it works...
> >>>>>
> >>>>> ________________________________
> >>>>>
> >>>>> From: hodak_at_chips.ncsu.edu [mailto:hodak_at_chips.ncsu.edu]
> >>>>> Sent: Tue 11/22/2005 4:00 AM
> >>>>> To: Michel Espinoza-Fonseca
> >>>>> Cc: vmd-l_at_ks.uiuc.edu
> >>>>> Subject: RE: vmd-l: Uncharged terminal ends?
> >>>>>
> >>>>>
> >>>>>
> >>>>> I cannot minimize the system (at least not with namd), since I
get that error
> >>>>> about HB CT1 HB angle parameters when I try to run namd with my
system.
> >>>>>
> >>>>> On Tue, 22 Nov 2005, Michel Espinoza-Fonseca wrote:
> >>>>>
> >>>>>> That's weird... Are you minimizing your system first ? Usually
I get the same thing you described (multiple bonds on the ACE or NME
terminals), but you can easily solve this problem by subjecting your
system to a short (~1000 steps) minimization.

> >>>>>>
> >>>>>> After that you should't have any problem.
> >>>>>>
> >>>>>> Hope it helps.
> >>>>>>
> >>>>>> Michel
> >>>>>>
> >>>>>> ________________________________
> >>>>>>
> >>>>>> From: owner-vmd-l_at_ks.uiuc.edu on behalf of hodak_at_chips.ncsu.edu
> >>>>>> Sent: Tue 11/22/2005 3:18 AM
> >>>>>> To: Justin Gullingsrud
> >>>>>> Cc: vmd-l_at_ks.uiuc.edu
> >>>>>> Subject: Re: vmd-l: Uncharged terminal ends?
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> This helped a lot. I decided that I want acetylated N-terminus
and
> >>>>>> methylated C-terminus. Using
> >>>>>>
> >>>>>> first ACE
> >>>>>> last CT1
> >>>>>>
> >>>>>> I can get the ends I want, although vmd shows extra bonds that
those added
> >>>>>> groups have carbons connected to N or C. I am not sure if this
is a
> >>>>>> problem or not.
> >>>>>> I went ahead and used generated psf and pdb files as input for
namd
> >>>>>> simulation, but I get the following error:
> >>>>>>
> >>>>>> FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HB CT1 HB
> >>>>>> ------------- Processor 0 Exiting: Called CmiAbort ------------
> >>>>>> Reason: FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HB CT1
HB
> >>>>>>
> >>>>>> Charm++ fatal error:
> >>>>>> FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HB CT1 HB
> >>>>>>
> >>>>>> The problem seems to be the C-terminal end, omitting "last CT1"
namd
> >>>>>> simulation runs without problems.
> >>>>>>
> >>>>>> Any idea what the problem is and how it can be solved?
> >>>>>>
> >>>>>> Thanks,
> >>>>>> Miro
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> On Mon, 21 Nov 2005, Justin Gullingsrud wrote:
> >>>>>>
> >>>>>>> Hi,
> >>>>>>>
> >>>>>>> You probably want an acetylated N terminus, then, which you
can get by
> >>>>>>> specifying "first ACE". I'm not sure what kind of C terminus
you're
> >>>>>>> looking for, but check out the PRES patches in the topology
file to
> >>>>>>> see what's available.
> >>>>>>>
> >>>>>>> Hope this helps,
> >>>>>>> Justin
> >>>>>>>
> >>>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>
> >>>
> >>>
> >>
> >>
> >
>